The story focuses on the Spartan-IIIs codenamed "Headhunters," following one of their top secret missions. It also contrasts the publically celebrated SPARTAN-IIs with a true black-ops unit of SPARTAN-IIIs. Only ONI Section Three operatives know the truth behind their existence.

The Headhunters were a top-secret group of SPARTAN-IIIs, "a secret, even to their peers." Their missions consisted of sabotage, assassination and other wetwork assignments too dangerous or sensitive for normal soldiers. Individuals completing the program were forced to survive two or more specially assigned training missions before being evaluated in the additional, grueling training regimen (seven months of supervised field exercises, followed by six months real-world wartime insertions). At the program's height there was a maximum contingent of six squads - six teams, with a total of seventeen soldiers rotating in to fill gaps whenever a SPARTAN was killed or wounded. Fireteams were comprised of two Headhunters, initially paired via exhaustive interviews and ONI profiling. Headhunters focuses on two such soldiers, Jonah and Roland. Their combat skills and teamwork were matched to 97.36 percent.

The fireteam's mission was to slip onto a Covenant-held moon (believed to be a dig-site for a hidden artifact), and remove six of the ten identified base camps situated around the outer perimeter of a much larger central compound. A second team of Headhunters would remove the remaining bases. The confusion and reshuffling of troops and supplies by the Covenant contingent following each base camp's dismantling proved to be the opening salvo in a full-scale assault by a dozen SPARTAN III fireteams with orbital backup.[2]

Roland and Jonah, armed with the latest experimental equipment including M7S Caseless Submachine Guns and M6C/SOCOM pistols, recon, infiltrate, and rig a Covenant digging site for demolition. The soldiers slipped past a perched Kig-Yar sniper, and into the camp, using VISR HUDs to target cloaked Elites. While the two soldiers are friends and comrades, Jonah in particular takes almost sadistic pleasure in killing Covenant. Roland serves as the more level-headed tactician of the Headhunters. After gathering intel for two days, they execute their plan. Roland, with an experimental active camouflage module, targeted the reactors in the base while Jonah ruthlessly hunted Covenant in the camp. The soldiers make full use of the new Energy Disruptor, a device that disables Covenant plasma weapons and energy shields. Taking the Unggoy, Kig-Yar, and Sangheili off guard, Jonah killed them with ease.

After Roland has set the charges using his av-cam, he regrouped with Jonah on the other side of the camp. Jonah takes full advantage of the Elite's sense of honor, using one of their severed heads to taunt the enemy. Together, the soldiers kill the remaining Covenant guards. Jonah disables the last Elite with two shots to the knees. In a rare subversion, the SPARTANs openly mock their 'honorable' enemies, ridiculing the hypocrisy and self-righteousness of their "holy" crusade to exterminate humanity. Jonah stabs the Elite in the neck before he can reply, unloading an entire clip from his pistol into the corpse out of spite. They are then caught off-guard by a squad of cloaked Spec-Op Elites. Roland is killed by an Energy Sword held by a Spec-Ops Sangheili wearing highly customized armor, and Jonah is surrounded by additional agents.

Jonah, showing no regard for his own life, mocked the Elite's cloaking devices refuting their claims that SPARTANs were cowards who struck from the shadows (an offense that would surely drive an Elite to a feral state, similar to looking a Jiralhanae in the eye). Jonah was attacked and severely injured—with the Elites content to toy with Jonah and planning his torture. This is uncommon as most Sangheili honorably kill their enemies instead of psychologically intimidating them. Having met his equal, Jonah realizes the importance of the Spec-Ops warriors due to their advanced technology, and is comforted by the thought of trading his one life for the six Sangheili sadists. Even after enduring the pain of an energy sword cutting out his eye, Jonah is able to release the trigger for the explosives that Roland rigged around the camp. The Covenant camp is vaporized, along with Jonah and the advanced Sangheili specialists.

In the story, there are many new examples of newly developed UNSC and Covenant technology, each of them being unique and useful in combat situations. Such examples of newly developed technologies are the VISR mode, the av-cam which is essentially the UNSC's first recreation of the Covenant's active camouflage technology and energy disruptors.

Halo: Reach features a new game type known as Headhunter in which the player must collect fallen skulls from their enemies.

The story heavily focuses on the various contradictions in the Elite's code of honor. The alien society is often bloodthirsty, striking from the shadows with cloaking devices with no regard for human 'vermin'. Unsurprisingly, the Sangheili are greatly offended when SPARTANs show them the same disrespect and cruelty.

There is a mistake in Section 6: Fair Trade. The sentence reads: "If the they got close enough to cut him...". It may be that the author accidentally tried to write "they" twice and forgot the Y.